{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:55:18Z","timestamp":1760057718298,"version":"build-2065373602"},"reference-count":32,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T00:00:00Z","timestamp":1740009600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ANO \u201cWilliam Harvey\u201d"},{"name":"NRC \u201cKurchatov institute\u201d"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), a causative agent of the COVID-19 disease, has been constantly evolving since its first identification. Mutations that are embedded in the viral genomic RNA affect the properties of the virus and lead to the emergence of new variants. During the COVID-19 pandemic, the World Health Organization has identified more than ten variants of the SARS-CoV-2 virus. Five of these\u2014Alpha, Beta, Gamma, Delta, and Omicron\u2014were classified as variants of concern (VOCs), as they caused significant outbreaks of the disease. Additionally, two progeny variants of Omicron, designated JN.1 and KS.1, are still causing new waves of infections. Due to the emergence of various SARS-CoV-2 variants, in some cases, it has become important to identify a particular variant in a sample. Here, we have developed a multiplexed probe-based real-time PCR system for the identification of SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, Omicron B.1.1.529\/BA.1, and Omicron BA.2), as well as modern Omicron variants JN.1 and KS.1. The sensitivity and specificity of the PCR system have been tested using isolated viral genomes and RNA preparations from human nasopharyngeal swabs. The system allows for rapid identification of coronavirus variants in the cryopreserved and fresh samples.<\/jats:p>","DOI":"10.3390\/ijms26051786","type":"journal-article","created":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T04:03:17Z","timestamp":1740024197000},"page":"1786","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Real-Time PCR-Based Test as a Research Tool for the Retrospective Detection and Identification of SARS-CoV-2 Variants of Concern in a Sample"],"prefix":"10.3390","volume":"26","author":[{"given":"Valeria O.","family":"Makarova","sequence":"first","affiliation":[{"name":"Moscow City Clinical Hospital Named after I.V. Davydovsky, 109240 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Artem","family":"Shelkov","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya\u201d of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0728-5478","authenticated-orcid":false,"given":"Anna","family":"Iliukhina","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya\u201d of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentin","family":"Azizyan","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya\u201d of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inna V.","family":"Dolzhikova","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya\u201d of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4111-0874","authenticated-orcid":false,"given":"Elena","family":"Vasilieva","sequence":"additional","affiliation":[{"name":"Moscow City Clinical Hospital Named after I.V. Davydovsky, 109240 Moscow, Russia"},{"name":"FSBEI HE \u201cRussian University of Medicine\u201d of the Ministry of Health of the Russian Federation, 127473 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1018-5195","authenticated-orcid":false,"given":"Alexey A.","family":"Komissarov","sequence":"additional","affiliation":[{"name":"Moscow City Clinical Hospital Named after I.V. Davydovsky, 109240 Moscow, Russia"},{"name":"FSBEI HE \u201cRussian University of Medicine\u201d of the Ministry of Health of the Russian Federation, 127473 Moscow, Russia"},{"name":"National Research Centre \u201cKurchatov Institute\u201d, 123182 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Khetran, S.R., and Mustafa, R. (2023). 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